Technically, xili-language since first release (3 years ago) uses a taxonomy named language with the querytag ‘lang’. To switch between languages and parts of a site, xili-language don’t use cookies. The plugin adds new sub-selection of posts according languages and changes the language (via switch of .mo) of the labels of the theme. Because designing is not data-design as mentioned in readme, the plugin don’t provide flags (but examples for webmaster or theme designer). More then 3 ways to create a language menu (via template tag, widget, and insertion in menus if location of menu exists) are available. xili-language is able to be set according content strategy and navigation rules.
In the case of Jon, the theme is in fact a commercial framework for webmaster not using php. The theme/tool don’t use powerful location menus. With little addons adapted to this framework theme, xili-language is working now.